DTC - I agree with you completely. Editing's not about interfering, it's often about offering a bit of restructuring. Similar to proof-reading - I've proofed stuff recently that isn't at all in my field of expertise, it's the grammar, structure and readability which was wanted. Not my place to change the context or the content.
I wouldn't change a section without consulting with the author first - what I'd do is suggest that "this might be better in this section" or "do you think this part is really relevant here"?
Since we don't know what your brief is, how could we comment on that? - this is the first time you've mentioned that your brief told you to "remove bits". How do you classify how big a "bit" is? I'd say a quarter of the text is far more than a bit.
All this speculation is a bit pointless really. Editors can be used for lots of reasons. The book's plot might be rubbish, or someone might see a quick way to take a turkey and turn it into a golden eagle.
But if the editor's remit is to make it publishable then he can basically do what he likes. And if the author doesn't like it he can try another publisher.
On the other hand, if you are proof reading for a friend you would not do that, But doesn't sound like that's the case here
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